Week 10

Mar 14 2022    
Week 10: Drs. Kara Bagot and Yaroslav Halchenko talk about ABCD Novel Technologies (the mobile, wearable, and social media data collected from ABCD Study participants) and ReproMan, the execution and environment manager.
Help and Resources: If you have questions about this week's material please post them to the ABCD-ReproNim Neurostars or the ABCD-ReproNim Slack.
Week 10 Assignments:


Week 10 Data Exercise: This week we ask that students complete a Data Exercise that asks questions about ABCD biospecimen measures and well reproducible workflows and analyses. Please complete the Week 10 Data Exercise after viewing the Week 10 videos. Solutions for this week’s data exercise can be found on our GitHub

Project Month Prep Data Exercise 1: Downloading, Inspecting, and Visualizing ABCD 4.0 Tabulated and Raw Behavioral Datasets: We are happy to release the first part of a three part series of Project Month Prep Data Exercises that provide step-by-step walkthroughs of how to download, inspect, visualize, and work with the ABCD 4.0 data release. The first Project Month Prep Exercise focuses on how to download and visualize the ABCD 4.0 Tabulated and Behavioral Datasets from the NDA. Next week we will release a second Project Month Prep Data Exercise that will focus on downloading ABCD 4.0 imaging data.

ABCD Data Access Confirmation: In order to access ABCD Study data you will need to obtain a Data Use Certification (DUC) from the NDA. We provide instructions on how to obtain ABCD data access to help with this process. Once you have an approved DUC please complete our ABCD Data Access Confirmation. Note that you do not need to have ABCD data access in order to take this course. This assignment is optional and does not count towards completion of the course. However, students who do not successfully complete this assignment will not be allowed to participate in Project Month.

ABCD-ReproNim JupyterHub Access Request: ABCD-ReproNim students with active DUCs can access to the new ABCD-ReproNim JupyterHub, a cloud-based scientific computing platform that is fully accessible through an internet browser (see this link for details about the JupyterHub project!) This document introduces the ABCD-ReproNim JupyterHub, how to access it, and outlines some basic usage rules. Students can use the Hub to work on Data Exercises and perform ABCD data analysis projects during the course. ABCD-ReproNim staff will grant access to students with active DUCs who submit an Access Request. Students without an active NDA Data Use Certification are invited to follow the instructions here where they can access the same computational environment locally via Docker.

AI/ML Course: If you are taking the parallel AI/ML Course you can view the videos for Week 3 here. If you would like to take the AI/ML Course then please make sure to register so we can add you to our AI/ML Course email list. Please note: we recommend that students first complete the main 12-week Course before beginning the 5-week AI/ML Course.

ReproNim Lecture: ReproMan – Execution and Environment Manager


Instructor Question and Answer Webcast Recording

Recorded in 2020. Note that course-related announcement made during this recording may be out of date. Please see the top of this page for 2022 Course announcements.

Week 10 Q&A Doc: Click here for written answers to the Q&A Doc.

Important Links and Platforms: